Cytogenetics is typically used for identifying structures such as balanced translocations, marker chromosomes, and other genomic structures present in a sample of interest. Examples of cytogenetics techniques include Giemsa (G) banding, M banding, or spectral karyotyping (SKY). However these technologies are generally low resolution, and are often limited to the spatial resolution of the light microscope, e.g., several megabases. In addition techniques, such as M-banding require manual microdissection of the chromosomes of interest, e.g., under a light or fluorescence microscope. Therefore, structures of interest such as duplications, inversions, or translocations need to be at least several megabases (Mb) in length. Furthermore accurate and reproducible determination of the boundaries of genomic structures is limited by the relatively low resolution of these current techniques. Accordingly, there is a need to improve the spatial resolution of mapping and characterizing genomic structures.